[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi Justin,

Can you please let me know the exact commands?

None of the commands which I tried are working...

Thanks,
Neha




On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/28/17 8:33 AM, Neha Gupta wrote:
>
>> Hi,
>>
>> I tried this one
>>
>> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
>> index.ndx
>>
>> This asks me to select a group fro clustering and then select a group for
>> output..
>>
>> What should I select first and then next?
>>
>
> Clustering isn't relevant. Your situation is much simpler than it's being
> made out to be.
>
> 1. Make molecules whole
> 2. Remove jumps
> 3. Center
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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